[English] 日本語
Yorodumi
- PDB-8cd3: Crystal structure of human Scribble PDZ1 domain in complex with h... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cd3
TitleCrystal structure of human Scribble PDZ1 domain in complex with human TMIGD1
Components
  • Protein scribble homolog
  • Transmembrane and immunoglobulin domain-containing protein 1
KeywordsPROTEIN BINDING / PDZ domain / cell polarity / Scribble / transmembrane protein
Function / homology
Function and homology information


extrinsic component of postsynaptic density membrane / establishment of T cell polarity / cochlear nucleus development / apoptotic process involved in morphogenesis / astrocyte cell migration / myelin sheath abaxonal region / Scrib-APC-beta-catenin complex / synaptic vesicle targeting / establishment of apical/basal cell polarity / polarized epithelial cell differentiation ...extrinsic component of postsynaptic density membrane / establishment of T cell polarity / cochlear nucleus development / apoptotic process involved in morphogenesis / astrocyte cell migration / myelin sheath abaxonal region / Scrib-APC-beta-catenin complex / synaptic vesicle targeting / establishment of apical/basal cell polarity / polarized epithelial cell differentiation / epithelial structure maintenance / neurotransmitter receptor transport, endosome to postsynaptic membrane / mammary gland duct morphogenesis / cell-cell contact zone / establishment or maintenance of epithelial cell apical/basal polarity / post-anal tail morphogenesis / activation of GTPase activity / protein localization to adherens junction / auditory receptor cell stereocilium organization / negative regulation of mitotic cell cycle / RND2 GTPase cycle / RND3 GTPase cycle / positive chemotaxis / regulation of postsynaptic neurotransmitter receptor internalization / receptor clustering / negative regulation of activated T cell proliferation / RHOJ GTPase cycle / RHOQ GTPase cycle / positive regulation of receptor recycling / CDC42 GTPase cycle / immunological synapse / synaptic vesicle endocytosis / signaling adaptor activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell-cell junction / cell junction / cell migration / presynapse / lamellipodium / basolateral plasma membrane / cell population proliferation / postsynaptic density / positive regulation of apoptotic process / cadherin binding / protein kinase binding / glutamatergic synapse / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat ...: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMaddumage, J.C. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1103871 Australia
CitationJournal: Commun Biol / Year: 2023
Title: Membrane recruitment of the polarity protein Scribble by the cell adhesion receptor TMIGD1.
Authors: Thuring, E.M. / Hartmann, C. / Maddumage, J.C. / Javorsky, A. / Michels, B.E. / Gerke, V. / Banks, L. / Humbert, P.O. / Kvansakul, M. / Ebnet, K.
History
DepositionJan 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Protein scribble homolog
A: Transmembrane and immunoglobulin domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)11,7472
Polymers11,7472
Non-polymers00
Water1,11762
1
B: Protein scribble homolog
A: Transmembrane and immunoglobulin domain-containing protein 1

B: Protein scribble homolog
A: Transmembrane and immunoglobulin domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)23,4944
Polymers23,4944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+1/2,y,-z-1/41
Buried area3500 Å2
ΔGint-11 kcal/mol
Surface area11840 Å2
Unit cell
Length a, b, c (Å)53.664, 53.664, 215.703
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-949-

HOH

21A-103-

HOH

-
Components

#1: Protein Protein scribble homolog / Scribble / hScrib / Protein LAP4


Mass: 10877.308 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q14160
#2: Protein/peptide Transmembrane and immunoglobulin domain-containing protein 1


Mass: 869.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 24% w/v PEG 1500, 20% Ethylene Glycol.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.9→43.01 Å / Num. obs: 13031 / % possible obs: 100 % / Redundancy: 26.1 % / Biso Wilson estimate: 30.37 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.7
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 809 / CC1/2: 0.921

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.01 Å / SU ML: 0.2124 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.8127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2225 659 5.07 %
Rwork0.1962 12344 -
obs0.1975 13003 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms809 0 0 62 871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011818
X-RAY DIFFRACTIONf_angle_d1.28381104
X-RAY DIFFRACTIONf_chiral_restr0.0793127
X-RAY DIFFRACTIONf_plane_restr0.0109147
X-RAY DIFFRACTIONf_dihedral_angle_d6.4011119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.050.24031350.19632389X-RAY DIFFRACTION99.8
2.05-2.250.19031100.16412433X-RAY DIFFRACTION100
2.25-2.580.23191220.17992445X-RAY DIFFRACTION100
2.58-3.250.20771380.20922464X-RAY DIFFRACTION100
3.25-43.010.22921540.2012613X-RAY DIFFRACTION99.96
Refinement TLS params.Method: refined / Origin x: 11.9646087635 Å / Origin y: -0.23275637232 Å / Origin z: -12.5611567071 Å
111213212223313233
T0.212287145933 Å2-0.0411703448049 Å20.00649696945074 Å2-0.272864976467 Å2-0.0206117855479 Å2--0.249265906448 Å2
L0.317988412529 °2-0.168183436364 °2-0.390769756866 °2-0.721289025899 °2-0.134731367841 °2--0.664043772467 °2
S0.0501548581327 Å °0.0859594845887 Å °0.0164795344445 Å °0.0185924838553 Å °-0.0669212354309 Å °0.16926651931 Å °0.0438629954547 Å °-0.089547761913 Å °-0.000598843734905 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more